Addressing issue #1

klamt-lab · Feb 4, 2020 · aebd131 · aebd131
1 parent 50f83e0
commit aebd131
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Showing 6 changed files with 5 additions and 5 deletions.
diff --git a/autopacmen/data_create_combined_kcat_database.py b/autopacmen/data_create_combined_kcat_database.py
@@ -40,7 +40,7 @@
 @click.option("--output_path",
               required=True,
               type=click.Path(exists=True, file_okay=True, dir_okay=True),
-              prompt="BRENDA JSON path",
+              prompt="Output path",
               help="Full path to the newly created combined JSON")
 def parse_create_combined_kcat_database(sabio_rk_kcat_database_path: str, brenda_kcat_database_path: str, output_path: str) -> None:
     """Combines the BRENDA and SABIO-RK JSONs into one big JSON which can be used by modeling_get_reactions_kcat_mapping.py

diff --git a/autopacmen/data_parse_brenda_textfile.py b/autopacmen/data_parse_brenda_textfile.py
@@ -66,7 +66,7 @@ def parse_brenda_textfile_cli(brenda_textfile_path: str, bigg_metabolites_json_f
     Load the BRENDA textfile 'C:\\folder\\download.txt' while the BIGG metabolites file
     is in 'C:\\bigg\\' and the newly generated JSON shall be named 'C:\\folder\\brenda.json'
     <pre>
-    python data_parse_bigg_metabolites_file.py --brenda_textfile_path C:\\folder\\download.txt --bigg_metabolites_json_folder C:\\bigg\\ --json_output_path C:\\folder\\brenda.json
+    python data_parse_brenda_textfile.py --brenda_textfile_path C:\\folder\\download.txt --bigg_metabolites_json_folder C:\\bigg\\ --json_output_path C:\\folder\\brenda.json
     </pre>
     """
     parse_brenda_textfile(brenda_textfile_path, bigg_metabolites_json_folder, json_output_path)

diff --git a/autopacmen/docs/manual.odt b/autopacmen/docs/manual.odt
diff --git a/autopacmen/modeling_create_smoment_model.py b/autopacmen/modeling_create_smoment_model.py
@@ -52,7 +52,7 @@
 @click.option("--excluded_reactions",
               required=False,
               type=str,
-              prompt="Name of output SBML",
+              prompt="Excluded reactions",
               help="Excluded reactions for which the pseudo-metabolite of the protein pool shall not be introduced. Must be semicolon-separated.")
 @click.option("--type_of_default_kcat_selection",
               required=True,

diff --git a/autopacmen/modeling_get_reactions_kcat_mapping.py b/autopacmen/modeling_get_reactions_kcat_mapping.py
@@ -101,7 +101,7 @@ def get_reactions_kcat_mapping_cli(sbml_path: str, project_folder: str, project_
     python modeling_get_reactions_kcat_mapping.py --sbml_path C:\\model\\test.xml --project_folder C:\\project\\ --project_name example --organism 'Escherichia coli' --kcat_database_path C:\\database\\database.json --protein_kcat_database_path C:\\database\\user.json --type_of_kcat_selection 'mean'
     </pre>
     """
-    get_reactions_kcat_mapping(sbml_path, project_folder, project_name, organism, kcat_database_path, protein_kcat_database_path)
+    get_reactions_kcat_mapping(sbml_path, project_folder, project_name, organism, kcat_database_path, protein_kcat_database_path, type_of_kcat_selection)
 
 
 # Start-up routine if script is called

diff --git a/setup.py b/setup.py
@@ -5,7 +5,7 @@
 
 setuptools.setup(
     name="autopacmen-Paulocracy",
-    version="0.5.2",
+    version="0.5.3",
     author="Paulocracy",
     author_email="bekiaris@mpi-magdeburg.mpg.de",
     description="The AutoPACMEN package",